Four months after buying the Wall Street Journal, Rupert Murdoch has been accused by a special independent committee of breaking "the letter and the spirit" of an agreement to protect editorial integrity.

A five-strong committee established as a condition of the Bancroft family's $5bn (£2.5bn) sale of the paper's Dow Jones parent company to Murdoch has complained that it was kept in the dark over the resignation of the Journal's top editor.

Committee members say they were not told until after the event about the controversial resignation last week of the managing editor, Marcus Brauchli, which has prompted fevered rumours of a rift over the direction of the paper.

"Although our charter does not directly envision a process for dealing with a resignation, committee members expressed the view that learning of the Brauchli matter after the fact failed to meet the letter and the spirit of the agreement," a statement released last night said.

The committee, chaired by the former Detroit News comment editor Thomas Bray, is supposed to be consulted over any changes in personnel among the top echelons of the Journal. Staff at the newspaper say that Brauchli, 46, quit because he felt he was being frozen out of decisions - particularly after Murdoch's appointment of the former Times editor Robert Thomson as publisher of the Journal.

Some staff are upset at efforts to curtail lengthy news features and to change the balance of coverage from business news to politics and general news. Brauchli was reportedly incensed that he was not told that the paper intended to begin printing its US edition in London.

In its statement, the committee said it was left powerless to intervene: "The committee met subsequently and decided there was no practical way to 'unresign' Brauchli and start the process over."

Members include the former Associated Press chief executive Louis Boccardi.

In spite of his resignation, Brauchli has accepted a job as a consultant to Murdoch's News Corporation. He told the Journal's website last night that he did not view it as necessary to report his "voluntary resignation" to the committee, but he added: "I regret that they first learned of my resignation late in the process."

A spokesman for the Journal declined to comment.

Murdoch's purchase of Dow Jones was agreed after a lengthy struggle among members of the Bancroft dynasty, some of whom feared that the Australian-born billionaire would not respect the paper's traditions. The committee was one of several concessions made by Murdoch. He also agreed to pay the Bancrofts' advisory fees and offered a seat on News Corp's board to a Bancroft family representative.

John Morton, a media analyst, said Murdoch had shown an adroit hand in circumventing the committee: "We knew from the beginning that the man who owns the place will end up doing what he wants."

The Journal's weekday circulation rose by 0.4% over the six months to March to 2.07m, which is second only to USA Today among American papers. Murdoch has made little secret of his desire for the Journal to take on the New York Times.